Changes of Quality of Minimally-Processed Pineapple (Ananas comosus, var. 'Queen Victoria') during Cold Storage: Fungi in the Leading Role - MDPI

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Changes of Quality of Minimally-Processed Pineapple (Ananas comosus, var. 'Queen Victoria') during Cold Storage: Fungi in the Leading Role - MDPI
microorganisms
Article
Changes of Quality of Minimally-Processed
Pineapple (Ananas comosus, var. ‘Queen Victoria’)
during Cold Storage: Fungi in the Leading Role
Charlène Leneveu-Jenvrin 1, *, Baptiste Quentin 1 , Sophie Assemat 2,3 , Mathilde Hoarau 2,3 ,
Jean-Christophe Meile 2,3 and Fabienne Remize 1
 1   QualiSud, Univ de La Réunion, CIRAD, Univ Montpellier, Montpellier SupAgro, Univ d’Avignon,
     2 rue J. Wetzell, F-97490 Sainte Clotilde, France; b.quentin2605@gmail.com (B.Q.);
     fabienne.remize@univ-reunion.fr (F.R.)
 2   CIRAD, UMR QualiSud, F-97410 Saint Pierre, La Réunion, France; sophie.assemat@cirad.fr (S.A.);
     meile@cirad.fr (M.H.); jean-christophe.meile@cirad.fr (J.-C.M.)
 3   QualiSud, Univ Montpellier, CIRAD, Montpellier SupAgro, Univ d’Avignon, Univ de La Réunion,
     F-34000 Montpellier, France
 *   Correspondence: charlene.leneveu@univ-reunion.fr
                                                                                                      
 Received: 6 December 2019; Accepted: 27 January 2020; Published: 28 January 2020                     

 Abstract: Minimally-processed pineapple stored under refrigerated conditions is highly perishable.
 We aimed to characterize the evolution of physicochemical, sensory and microbiological quality
 during cold storage. Pineapple batches were sampled from several locations in Reunion Island and
 then minimally processed. In the processing step, the variability of firmness and counts of yeasts
 and molds were observed. Moreover, correlations between the sampling season and pH and b* color
 component, as well as between fungal population and b* parameter were observed. During storage,
 the visual aspect of pineapple cuts changed to brown and shiny, whereas olfactive descriptors shifted
 from fruity descriptors and fresh to fermented, alcoholic and milky. The values for pH, TA and TSS
 did not significantly vary according to storage time. A decrease in firmness and C* color parameter
 was observed. Yeast and mold counts were significantly higher after 7 days of storage. The diversity
 in yeasts and molds was mainly dependent on the considered batches observed from PCR-DGGE
 profiles. Fungal species were isolated from spoiled pineapple cuts. The implication of Penicilllium
 citrtrinum, Talaromyces amestolkiae, Rhodotorula mucilaginosa, Saccharomyces cerevisiae, and Meyerozyma
 caribbica in the spoilage of minimally-processed pineapple cuts was further demonstrated.

 Keywords: fruit; microbiological quality; sensory quality; fresh-cut

1. Introduction
     Fruit and vegetable consumption has considerably increased in the past decade. In fact, they have
now become an essential part of the human diet. Pineapple (Ananas comosus) is appreciated for its taste
and juiciness. It presents many nutritional benefits, being a good source of antioxidants, especially
polyphenols, minerals, vitamin C, vitamin A, and vitamin B6 [1,2].
     Minimally-processed fruits are attractive for consumers as they are perceived as healthy, fresh
and convenient for use [3]. However, their shelf-life is short, typically a few days under refrigeration,
because of physiological and microbiological disorders resulting from cutting the fruit.
     Many attempts have been made to increase minimally-processed pineapple shelf-life [4].
Controlled storage temperature and modified atmosphere packaging are the most used technologies
to preserve the quality of minimally-processed fruit [5–9]. Edible coatings can also prolong its
shelf-life [7,10]. Physical treatments, such as UV-C, heat, ultrasound or high pressure inert gas,

Microorganisms 2020, 8, 185; doi:10.3390/microorganisms8020185          www.mdpi.com/journal/microorganisms
Changes of Quality of Minimally-Processed Pineapple (Ananas comosus, var. 'Queen Victoria') during Cold Storage: Fungi in the Leading Role - MDPI
Microorganisms 2020, 8, 185                                                                                                      2 of 17

 to preserve the quality of minimally-processed fruit [5–9]. Edible coatings can also prolong its shelf-
Microorganisms 2020, 8, 185                                                                                                        2 of 18
 life [7,10]. Physical treatments, such as UV-C, heat, ultrasound or high pressure inert gas, successfully
 enhanced the shelf-life of minimally-processed pineapple [11–14]. These treatments probably affected
 fruit enzymeenhanced
successfully        activitiesthe involved
                                      shelf-life in ofthe   respiration rate, browning
                                                         minimally-processed          pineapple  and    metabolism
                                                                                                    [11–14].      These of     phenolic
                                                                                                                            treatments
 compounds.
probably           Thefruit
             affected    growth
                              enzyme of microorganisms,
                                          activities involvedeither  in thethe    natural rate,
                                                                             respiration    florabrowning
                                                                                                   [7,10], yeasts       isolated from
                                                                                                                 and metabolism         of
 spoiled     pineapple      [6]  or    foodborne         pathogens      [10]   was    modulated       by
phenolic compounds. The growth of microorganisms, either the natural flora [7,10], yeasts isolated from    the     above-mentioned
 treatments.
spoiled   pineapple [6] or foodborne pathogens [10] was modulated by the above-mentioned treatments.
       The impact
       The   impact of of these
                           these technologies
                                  technologies was    was also
                                                             also determined
                                                                   determined on   on respiration
                                                                                      respiration rate,
                                                                                                      rate, firmness
                                                                                                             firmness degradation
                                                                                                                          degradation
 and   color    changes,     especially     for   L*   and    b*,  which    decrease    reveals
and color changes, especially for L* and b*, which decrease reveals translucency of fruit pieces   translucency        of  fruit[5,7,12].
                                                                                                                                  pieces
 [5,7,12]. However,       above    all, special   attention     was   paid  to  sensory    properties
However, above all, special attention was paid to sensory properties and volatile compounds involved     and   volatile    compounds
 involved
in            in the pineapple
    the pineapple      aroma [2].aroma From [2].     From sixcultivars,
                                                six different      different 83cultivars,
                                                                                   volatile83   volatile compounds,
                                                                                             compounds,         including including
                                                                                                                              15 esters
 15  esters  and   57 alkenes,    were     detected     [2].  Different   volatile  compounds
and 57 alkenes, were detected [2]. Different volatile compounds were shown to be involved            were   shown      to be involved
                                                                                                                                  in the
 in the[2,6,8].
aroma      aromaDuring[2,6,8].theDuring
                                     storagethe      storage of minimally-processed
                                                 of minimally-processed            pineapple, anpineapple,
                                                                                                      increase inan        increase in
                                                                                                                       concentration
 concentration
of                  of ethanol,
    ethanol, ethylacetate,            ethylacetate,and
                                 acetaldehyde,            acetaldehyde,
                                                              methyl esters   and   methyl esters
                                                                                 of carboxylic    acidsofwascarboxylic
                                                                                                                 noticed in  acids   was
                                                                                                                                several
 noticed    in  several    studies    [6,8,15].    However,        some   discrepancies      were
studies [6,8,15]. However, some discrepancies were observed in other volatile compounds detected,    observed       in  other   volatile
 compounds
possibly          detected,
           in relation           possibly
                         to cultivar           in relation
                                        or storage     conditions.to cultivar
                                                                      The increaseor in
                                                                                      storage    conditions.
                                                                                         concentration              The compounds
                                                                                                           of volatile      increase in
 concentration      of  volatile    compounds          observed      during    storage   can
observed during storage can result either from living tissue metabolism or production by yeastsresult   either    from    living   tissue
                                                                                                                                      [6].
 metabolism       or  production        by   yeasts    [6].  The    main   difference     in  samples
The main difference in samples stored under different conditions was attributed to a sensory panel        stored     under     different
 conditions
to              was attributed
    odor, especially      with theto“fermented”
                                         a sensory panel        to odor,[6].
                                                           descriptor      especially
                                                                              However,  withWutheet “fermented”
                                                                                                     al. (2012) [11]descriptor
                                                                                                                          noticed that[6].
 However,       Wu  et al.  (2012)   [11]  noticed      that  most   differences    were    detected
most differences were detected in appearance and flavor between control and high-pressure treated      in  appearance        and   flavor
 between control
pineapple      cuts. and high-pressure treated pineapple cuts.
       The   present
       The present studystudy aimed
                                 aimed to   todescribe
                                                describethe  theinitial
                                                                   initialphysicochemical,
                                                                           physicochemical, sensory
                                                                                                  sensory and  and microbiological
                                                                                                                     microbiological
 qualities   of  minimally-processed           ‘Queen      Victoria’   pineapple     and
qualities of minimally-processed ‘Queen Victoria’ pineapple and their changes upon storage their changes      upon    storageat   at44°C.
                                                                                                                                      ◦ C.

AAfocus
    focuswas
           wasput putononthethe diversity
                                diversity of  of yeasts
                                                  yeasts andand molds
                                                                   molds and
                                                                           and the
                                                                                 the modulation
                                                                                     modulation of   of the
                                                                                                         the encountered
                                                                                                               encountered species
                                                                                                                                 species
 according     to the  sample    and     the
according to the sample and the storage time. storage     time.

2. Materials
2. Materials and
             and Methods
                 Methods

2.1.
2.1. Fruits
     Fruits Preparation
            Preparation
     ‘Queen
       ‘QueenVictoria’
                Victoria’pineapples
                           pineappleswere
                                       werecollected  from
                                              collected     different
                                                         from         locations
                                                               different        in Reunion
                                                                          locations          Island
                                                                                    in Reunion       (Figure
                                                                                                   Island     1) over
                                                                                                           (Figure 1)
2over
  years2(2017–2019).    LocationsLocations
           years (2017–2019).      mostly differed
                                              mostly in differed
                                                        their annual
                                                                   in rainfall: West location
                                                                       their annual   rainfall:isWest
                                                                                                   characterized
                                                                                                         locationby is
very  low rainfall
 characterized    by(500–1000
                      very lowmm),   South
                                rainfall     and North
                                         (500–1000    mm),locations  by moderate
                                                             South and             rainfall (1250–2000
                                                                          North locations    by moderate   mm),  and
                                                                                                              rainfall
East locationmm),
 (1250–2000     by veryandhigh rainfall
                            East        (2000–3000
                                  location  by verymm). highAverage
                                                              rainfall daily solar radiation
                                                                        (2000–3000              is high (1700–2100
                                                                                     mm). Average        daily solar
J/cm 2 ) in all locations.   In Reunion
 radiation  is high  (1700–2100  J/cm²) inIsland,   only two
                                            all locations.      seasonsIsland,
                                                           In Reunion     are observed:
                                                                                 only twowinter
                                                                                           seasonsfrom      April to
                                                                                                       are observed:
September,
 winter fromand    summer
                April        from October
                       to September,         to March.
                                      and summer       from October to March.

      Figure1.1.Map
      Figure      Mapof Reunion IslandIsland
                         of Reunion    with sampling   locationslocations
                                              with sampling      (black stars). Fourstars).
                                                                            (black   locations were
                                                                                            Four    differentiated
                                                                                                  locations   were
      based on annual
      differentiated    cumulative
                     based          rainfall
                            on annual        on yearrainfall
                                       cumulative    2017. Source:
                                                             on yearMeteo   France. Meteo France.
                                                                      2017. Source:
Changes of Quality of Minimally-Processed Pineapple (Ananas comosus, var. 'Queen Victoria') during Cold Storage: Fungi in the Leading Role - MDPI
Microorganisms 2020, 8, 185                                                                        3 of 18

     For each sampling date and origin, at least three pineapples with similar maturity levels were
picked up (Table 1).

              Table 1. Pineapple sample names, sampling location and month of sampling (season).

                              Samples        Location                  Date
                                V0             East           October 2017 (summer)
                               CP1             East           March 2018 (summer)
                               VSA             East             May 2018 (winter)
                               CP3             East             June 2018 (winter)
                               VSA2            East             June 2018 (winter)
                               VET             East             July 2018 (winter)
                               VRO             East             July 2018 (winter)
                               VGA             East             July 2018 (winter)
                               CP01            West           October 2017 (summer)
                               CP02            West           October 2017 (summer)
                                V3             West           March 2018 (summer)
                               CP2             West             April 2018 (winter)
                                V5             West             April 2018 (winter)
                               VSL             West             May 2018 (winter)
                                V7             West             May 2018 (winter)
                               VSL2            West             June 2018 (winter)
                               CP03           North         December 2017 (summer)
                                BP             South          March 2018 (summer)
                                V1             South          March 2018 (summer)
                                V2             South          March 2018 (summer)
                                V4             South            April 2018 (winter)
                                V6             South            May 2018 (winter)
                               TP1             Any            January 2019 (summer)
                               TP2             Any           February 2019 (summer)
                               TP3             Any              May 2019 (winter)

     In addition, three samples were collected from a local producer of minimally-processed fruit and
vegetables (Table 1).
     Within 24 h after collection, the fruits were manually peeled and cut into pieces of ca. 3 × 2 cm.
Pieces from different pineapples were manually mixed and further shared into commercial freezer
bags. Each bag contained ca. 100 g of fruit and was stored at 4 ◦ C until analysis. One bag was used for
each time point of analysis.

2.2. Fruit Quality Determination

2.2.1. Microbiology
     Prior to analysis, 30 g of fruits were collected from freezer bags and mixed with 30 mL of SPW
(saline peptone water, Condalab, Torrejón de Ardoz, Madrid, Spain) in a stomacher for 1 min at
maximal speed. For microbial analysis, serial decimal dilutions were performed in SPW. Enterobacteria
were enumerated on VRBG agar (Biokar diagnostic, Solabia, Allonne, France) after incubation for 48 h
Microorganisms 2020, 8, 185                                                                        4 of 18

at 37 ◦ C. Psychrotrophic bacteria were enumerated on nutrient agar (Merck, Darmstadt, Germany)
incubated for 3 days at 10 ◦ C. Yeasts and molds enumeration was performed on Sabouraud glucose
agar with 100 mg/L chloramphenicol (Biokar diagnostic, Solabia, Allonne, France) after incubation at
30 ◦ C for 5 days. Yeast and molds were isolated under the same conditions.

2.2.2. Physicochemical
      pH value was measured by a pH meter (5231 Crison, and pH-meter Model GLP22, Crison Instruments
S.A. Barcelona, Spain), and the titratable acidity (TA) was determined by titration with 0.05 M NaOH
(TitroLine easy, Schott, Mainz, Germany). TA was expressed as citric acid equivalents in g/100 mL.
      Pineapple total soluble solids (TSS), expressed as Brix degrees (◦ Brix), were determined with a
hand refractometer (Atago, Tokyo, Japan) at room temperature.
      Three color determinations were performed for each sample (12 mL of mixture) with a
spectrophotometer CM 3500d (Minolta® , Carrières-sur-Seine, France). Measured color parameters
were L*, a* and b*. Numerical values of a* and b* were converted into a saturation variable or chroma:
                                                      q
                                               C∗ =       (a ∗2 +b∗2 )                                (1)

and in a measure of chromaticity, the hue angle:

                                              h◦ = arctan(b ∗ /a∗)                                    (2)

      Color difference:              q
                              ∆E =       (L ∗e −L∗c )2 + (a ∗e −a∗c )2 + (b ∗e −b∗c )2                (3)

in which L*e , a*e and b*e refer to the assay condition; and L*c , a*c and b*c to the control condition,
which was calculated with the initial color as control.
     Texture analysis was performed with a TA-TX2® texture analyzer (Stable Micro Systems Ltd.,
Godalming, UK) equipped with a 5 kg load cell. A 2-mm diameter rod was used to penetrate the
pineapple wedge sample at a test speed of 0.5 mm/s. The maximum penetration force was measured
and taken as firmness (N). Three pieces of pineapple were randomly withdrawn from each bag to carry
out repeats.

2.3. Spoilage Assays
     Nine fungal isolates were collected from pineapple cuts and identified (Table 2). Their ability to
spoil commercial pineapple juice (pasteurized, LawLam® ) was assayed by the inoculation of juice
and observation of changes during storage. Ten milliliters of juice were inoculated with ca. 4.6 log
CFU/mL of each fungal isolate and stored for 7 days at 4 ◦ C. Fungal enumeration and observation of
color modification, gas production and off-odors production were performed to detect spoilage activity.
This detection was performed in triplicate.
     To confirm the ability of each isolate to spoil minimally-processed pineapple, selected isolates
were separately prepared and used for inoculation. Pineapple cuts were dipped in an aqueous solution
containing ca. 4.6 log CFU/mL of fungal spoilage cocktail (1:2 w/v) for 5 min at 150 rpm. Afterwards,
they were drained and packaged (100 ± 2 g) in freezing bags and stored for 7 days at 4 ◦ C. Fruit quality
was then determined.
Microorganisms 2020, 8, 185                                                                                        5 of 18

                                         Table 2. Identification of fungal isolates.

                                                 Sampling      Fragment      Identity                  Accession
       Name             Identification                                                   E-Value
                                                  Source          (pb)         (%)                     Number
         R           Penicillium citrinum        VSL-D14           339          98      6.0 × 10−134   MN046972.1
         S           Penicillium citrinum        VSA-D14           426         100           0.0       MN653150.1
         A         Rhodotorula mucilaginosa      CP1-D7            234         100      2.0 × 10−117   MN535021.1
         C         Saccharomyces cerevisiae       BP-D3            507          99      1.0 × 10−161   MN244399.1
         D           Meyerozyma caribbica         V2-D7            330         100      1.0 × 10−170   MN658754.1
         F           Meyerozyma caribbica        VSL-D3            268          99      6.0 × 10−133   MN658754.1
         H           Meyerozyma caribbica        CP1-D3            320         100      4.0 × 10−165   MN416286.1
          I          Meyerozyma caribbica         BP-D3            274         100      1.0 × 10−139   MN658754.1
         20         Talaromyces amestolkiae       TP1-D3           159         95.6     4.0 × 10−64    MN549518.1

2.4. Sensory Quality Characteristics
     Sensory quality of ripe pineapple cuts was carried out by a panel of trained judges. Pineapple
cuts were placed at room temperature 1 hour before sensory analysis. Three pieces per sample were
randomly served and arranged on the plate for evaluation. Each sample was coded differently, with a
three-digit code.
     Descriptive profiles were determined for each sample. Preliminary sessions enabled to generate a
descriptive pineapple vocabulary. An 11-point scale between 0 and 10 was used to rate the intensity
of the different sensory criteria. The ISO 11035 (Sensory analysis—Identification and selection of
descriptors for establishing a sensory profile by a multidimensional approach) method was employed.
     Two distinct tests were used to determine if there was a detectable difference between two products
A and B: the two/five test and the triangle test. In the two/five test, samples from the same batch stored
for 0, 3, 7 or 14 days were compared. The triangle test was used to compare the control sample and
sample treated with the selected fungal cocktail, both after 7 days of storage according to the sensory
method described by ISO 4120-2004 (Sensory analysis–Methodology–Triangle test).

2.5. Molecular Biology Methods

2.5.1. DNA Extraction
    DNA was extracted for each pineapple sample from the SPW suspension prepared for microbial
counting. To achieve extraction, 2 mL of the suspension (stored at −80 ◦ C) were collected in two
microtubes and centrifuged at 14,000× g during 2 min. DNA extractions were carried out on the
assembled pellets according to procedure described by MP Biomedicals® (llkirch, France) with the
FastDNA kit and the FastPrep-24 Instrument using Lysing Matrix A and Lysis buffer CL-Y.

2.5.2. PCR-Denaturing Gradient Gel Electrophoresis (DGGE)
      The following DNA primers were used to amplify a region of the fungal ITS: GC-ITS1F
(CGCCCGCCGCGCGCGGCGGGCGGGGCGGGGGCACGGGGGGCTTGGTCATTTAGAGGAAGTAA)
and ITS4 (TCCTCCGCTTATTGATATGC) primers [16]. A 40-pb GC-clamp was added to the forward
primer in order to ensure that the fragment of DNA remains partially double stranded and that the
region screened is in the lowest melting domain [17].
      PCR amplification reaction was performed in a final volume of 50 µL containing 0.6 µM of
each primer, all the deoxyribonucleotide triphosphate (dNTPs) at 200 µM, 2 mM of MgCl2 , 10 µL of
5X Taq reaction buffer (Promega, Charbonnières-les-Bains, France), 1.25 U of Taq DNA polymerase
(Promega), and 1 µL of extracted DNA. PCR amplification reactions were carried out as follows: an
initial denaturation at 95 ◦ C for 2 min, 40 cycles at 95 ◦ C for 15 s, 57 ◦ C for 30 s and 72 ◦ C for 45 s,
and final extension at 72 ◦ C for 5 min. The PCR reactions were performed in a Thermocycler (Veriti,
Applied Biosystems, Thermo Fisher Scientific, Loughborough, UK). Aliquots (5 µL) of PCR products
were checked by electrophoresis migration in 2% (w/v) agarose gel with 1× TAE buffer (40 mM Tris-HCl
Microorganisms 2020, 8, 185                                                                             6 of 18

pH 7.4, 20 mM sodium acetate, 1.0 mM Na2 -EDTA). After running at 100 V for 45 min, the gels were
stained with ethidium bromide solution (50 µg/mL in TAE 1×) and quantified using a standard (DNA
mass ladder 100 bp, Promega).
      The PCR products were separated by DGGE using a Cleaver Scientific system (Cleaver Scientific,
Rugby, Warwickshire, UK). Briefly, 30 µL of PCR amplicons were loaded onto 8% (w/v) polyacrylamide
gels (acrylamide: N,N-methylene bisacrylamide, 37.5:1, Promega) in 1× TAE buffer (40 mM Tris-HCl
pH 7.4, 20 mM sodium acetate, 1.0 mM Na2 -EDTA). Electrophoresis was performed at 60 ◦ C using a
denaturing gradient ranging from 40% to 70% (100% corresponded to 7 M urea and 40% v/v formamide,
Promega). The gels were run at 20 V for 10 min and then at 80 V for 16 h. After electrophoresis, the gels
were stained for 1 h with ethidium bromide solution (50 µg/mL in 1× TAE), rinsed for 1 h in distilled
water, and then photographed on a UV transilluminator (Bio-Rad, Marnes-la-Coquette, France). Bands
of interest were cut, and the DNA was extracted. Electrophoretic profiles were analyzed with Phoretix
1D Pro software (Totallab, Newcastle-Upon-Tyne, UK), which considers band presence and relative
intensity on the line. Nearest Neighbor algorithm and Pearson coefficient correlation were used to
build the dendrogram.
      Detected bands were cut from the DGGE gel with a sterile scalpel as described previously [18].
Briefly, the DNA of each band was then eluted in 100 µL of TE buffer (10 mM TrisHCl; 1 mM EDTA;
pH 7.4, Sigma-Aldrich, Lyon, France) at 4 ◦ C overnight. DNA was precipitated by adding 1/10 volume
of sodium acetate (3 M, pH 5), 1µL of glycogen (Molecular Grade, Roche Diagnostics, Meylan, France),
and 300 µL of isopropanol and centrifuged at 15,000× g for 30 min at 4 ◦ C. The supernatant was
discarded, DNA pellets were washed with 500 µL 70% ethanol and after 5 min of centrifugation, the
DNA pellets were air dried for 1 h. Finally, the DNA was re-suspended in 20 µL of ultrapure water
and stored at −20 ◦ C.

2.5.3. Identification
      DNA primers ITS1F (CTTGGTCATTTAGAGGAAGTAA) and ITS4 were used to amplify a region
of the fungal ITS [16]. PCR amplification reaction was performed in a final volume of 50 µL containing
0.3 µM of each primer, all the deoxyribonucleotide triphosphate (dNTPs) at 200 µM, 1.5mM of MgCl2 ,
10 µL of 5× Taq reaction buffer (Promega), 1.5 U of Taq DNA polymerase (Promega), and 1 µL of
extracted DNA. PCR amplification reactions were carried out as follows: an initial denaturation at 95
◦ C for 2 min, 40 cycles at 95 ◦ C for 15 s, 53 ◦ C for 30 s and 72 ◦ C for 45 s, and final extension at 72 ◦ C

for 5 min. The PCR reactions were performed in a Thermocycler (Veriti, Applied Biosystems, UK).
Aliquots (5 µL) of PCR products were analyzed by electrophoresis in 2% (w/v) agarose gel with 1× TAE
buffer (40mM Tris-HCl pH 7.4, 20mM sodium acetate, 1.0mM Na2 -EDTA).
      After running at 100 V for 45 min, the gels were stained with ethidium bromide solution (50 µg/ mL
in TAE 1×) and quantified using a molecular weight marker (100 bp DNA ladder, Promega).
      The PCR products were sent to Macrogen (Amsterdam, The Netherlands) for sequencing. For each,
purification was applied, and sequencing was carried out on PCR products using ITS1F or ITS4 primers.
The sequences obtained were aligned with BioEdit software (Sequence Alignment Editor version
7.1.3.0, Freeware Copyright 1991–2007 Tom Hall) followed by a BLAST similarity search.

2.6. Statistical Analysis
     The XLSTAT software (Addinsoft, Paris, France) was used for statistical analyses.
     One-way variance analysis (ANOVA) was performed with a p-value of 0.001. The Ryan-Einot-
Gabriel-Welsh F (REGWQ) test was used for pair-wise comparisons.
     A correlation test for quantitative variables was performed with Kendall’s tau coefficient with a
p-value of 0.05. The correlation between one quantitative and one qualitative variable was investigated
with the biserial correlation method, using the Monte-Carlo simulation.
     Word cloud was used to visualize the frequency of descriptors chosen by the panel for samples with
the same duration of cold storage: Word font size is proportional to frequency. K-means classification
Microorganisms 2020, 8, 185                                                                                              7 of 18

was used to gather samples into classes according to their description with quantitative variables.
Two-dimension principal component analysis (PCA) plot was used to represent variables (olfactive
descriptors), observations (minimally-processed pineapple stored for 0, 3, 7 or 14 days) and their
relatedness and distance.

3. Results

3.1. Freshly Prepared Minimally-Processed Pineapple Characteristics
     A sensory analysis was performed to assign descriptors to freshly minimally-processed samples.
The major color descriptor was “yellow”, and olfactive descriptors were, in descending order of
frequency of occurrence, “pineapple”, “fresh”, “fruity”, “pomegranate”, “red fruit”, “citrus”, and
“sugared”. These olfactive descriptors are primarily related to fruity characteristics. This is consistent
with previous studies showing the role of methyl esters and lactones in the typical fruity flavor of
pineapple [19,20].
     The 25 pineapple batches were independently minimally-processed. For each, pH, TA, TSS,
firmness, L*, a*, and b*, color parameters were determined on the day of processing. Psychrotrophic
bacteria, enterobacteria, as well as yeasts and molds were counted. Table 3 shows mean values and
data dispersion between batches.

     Table 3. Values and dispersion of physicochemical parameters and microbiological counts of
     minimally-processed pineapple batches.

                                                                            Standard         Minimum          Maximum
                    Parameter                        Mean           ±
                                                                            Deviation         Value            Value
                      pH                              3.44          ±          0.27             3.09              4.20
                TA (g/100 mL)                         0.87          ±          0.20             0.68              1.33
                  TSS (◦ Brix)                        14.6          ±           1.5             11.1              17.8
                      L*                              36.7          ±           6.6             32.1              65.3
                      a*                              10.3          ±           2.1              6.3              13.3
                      b*                              50.4          ±           5.7             38.8              59.7
                    Chroma                            51.5          ±           5.6             39.6              60.2
                  Hue angle                           11.6          ±           2.5              6.3              15.3
                 Firmness (N)                          3.8          ±           1.2              2.0               6.7
     Psychrotrophic bacteria (log CFU/g)               3.7          ±           0.6             3.3 1              5.4
         Enterobacteria (log CFU/g)                   3.8           ±           0.6             3.0 2              5.3
         Yeasts & Molds (log CFU/g)                    4.4          ±           0.7              3.0               5.8
      1and 2 : the indicated values correspond to the detection level. For psychotropic bacteria, 14 batches showed counts
      below this level. For enterobacteria, four batches showed counts below this level.

     The pH values varied between 3.09 and 4.20, and 64% of them ranged between 3.3 and 3.8. Similarly,
for TA, 68% of values were in the range 0.73 and 0.98 g/100 mL. The values for pH, TA, and TSS were
in accordance with previously published data of carbohydrate content of pineapple [1,2,7,10,21,22].
     Firmness range was large, from 2.0 to 6.7 N. Among all parameters, firmness exhibited the highest
variation coefficient, of 32%. This range is in accordance with literature data.
     For the L* parameter, except for one extremely high value, all batches exhibited values below 41.6.
On the opposite, a* values were spread on the whole range, whereas 85% of b* values were above
45. As a consequence, C* and h◦ exhibited a Normal distribution, with p-values, calculated with the
Anderson-Darling test, of 0.53 and 0.23, respectively.
     Counts of psychrotrophic bacteria were for most batches below the detection limit. However,
five batches exhibited counts above 4 log CFU/g. For yeasts and molds, 72% of batches exhibited
counts above 4 log CFU/g, and 16% above 5 log CFU/g. Eventually, for enterobacteria, 40% of batches
exhibited counts above 4 log CFU/g, and 8% above 5 log CFU/g. The highest counts were thus observed
for yeasts and molds.
Microorganisms 2020, 8, 185                                                                                8 of 18

      Correlations between independent quantitative variables (pH, TA, TSS, microbial counts, L*, a*,
b*, firmness) were searched with the non-parametric Kendall test. A positive correlation between L*
and psychrotrophic bacteria enumeration was detected with a p-value of 0.028 and a Kendall’s tau
coefficient of 0.345. Two negative correlations, between pH and L* and between yeast and mold counts
and b*, were detected with p-values of 0.021 and 0.044 and coefficients of -0.336 and -0.291, respectively.
Surprisingly, no correlation was pointed out between TA and TSS, which evolve in an opposite way
during fruit ripening.
      Eventually, correlations were searched between qualitative (season and location of sampling) and
quantitative variables. Biserial correlation tool showed a correlation between season and pH, with a
p-value of 0.0002 and a coefficient of 0.60, and a correlation between season and b*, with a p-value of
0.015 and a coefficient of 0.49. This grouping is visualized from pineapple batches plotted on a graph
with x-axis being b* and y-axis being pH (Figure 2).
      Harvesting season has considerable impacts on the post-harvest quality of pineapple, affecting
internal browning and storage life [19]. The correlation between season and pH is not surprising but
could have been expected also with TA and TSS. Pineapple flesh color, especially b* and C*, TSS, TA,
and pH were influenced by the season in Thailand (three seasons: summer, rainy and winter) for the
Smooth Cayenne cultivar [23]. The importance of pre-harvest factors on post-harvest quality was
underlined by Chen et al. (2009) [24]. Whereas a model has been proposed to predict TSS of ‘Queen
Victoria’ pineapple flesh from agroclimatic conditions of Reunion Island [21], no correlation has8 been
Microorganisms 2020, 8, 185                                                                                  of 17
previously pointed out between pH, b* color parameter and season, for this cultivar or crop location.
      The relationship
      The   relationshipbetween
                              betweenpH pH
                                         and L*
                                              and could
                                                     L* be explicated
                                                         could         by different
                                                                 be explicated   bypineapple
                                                                                     differentflesh compositions,
                                                                                                 pineapple  flesh
which   are  reflected    on  these two   parameters.    Pineapple   flesh color depends  on  its
compositions, which are reflected on these two parameters. Pineapple flesh color depends on its   composition   in
carotenoids   and  flavonoids,    and the  content  in those compounds    was  showed to depend
composition in carotenoids and flavonoids, and the content in those compounds was showed to       on agroclimatic
conditions
depend    on [25].   Moreover,
              agroclimatic         the color[25].
                               conditions     of flavonoids
                                                   Moreover, depends
                                                               the coloron
                                                                         of the pH. By depends
                                                                            flavonoids  contrast, on
                                                                                                   explaining
                                                                                                      the pH. the
                                                                                                               By
correlations   between      a color parameter   and   a microbial  count  would  require extensive
contrast, explaining the correlations between a color parameter and a microbial count would require metabolomic
analyses to
extensive     find out which
            metabolomic           compounds
                              analyses  to find would   be implied.
                                                out which    compounds would be implied.

     Figure 2.
     Figure    Relationshipbetween
            2.Relationship   betweenseason
                                     seasonand
                                            andthe
                                                 theparameters
                                                     parameterspH
                                                                pHand
                                                                    andb*
                                                                        b*from
                                                                            fromfresh
                                                                                 freshminimally-processed
                                                                                       minimally-processed
     pineapple. Black circle: summer; white triangle: winter. Confidence ellipses correspond to the seasons.
     pineapple. Black circle: summer; white triangle: winter. Confidence ellipses correspond to the
     seasons.

3.2. Minimally-Processed Pineapple Changes over Refrigerated Storage
    Sensory descriptive profiles (olfactory and aspect) were established on minimally-processed
pineapple during refrigerated storage, after 3, 7, 10, and 14 days, and compared to freshly processed
samples (Figure 3).
Microorganisms 2020,
          Figure     8, 185
                 2. Relationship between season and the parameters pH and b* from fresh minimally-processed               9 of 18
          pineapple. Black circle: summer; white triangle: winter. Confidence ellipses correspond to the
          seasons.
3.2. Minimally-Processed Pineapple Changes over Refrigerated Storage
    3.2. Minimally-Processed
     Sensory                 Pineapple(olfactory
              descriptive profiles     Changes over
                                                 andRefrigerated Storageestablished on minimally-processed
                                                       aspect) were
pineapple  duringdescriptive
        Sensory    refrigerated storage,
                             profiles     after 3,and
                                      (olfactory   7, 10,  and 14
                                                        aspect)    days,
                                                                were     and compared
                                                                      established       to freshly processed
                                                                                  on minimally-processed
samples  (Figure
    pineapple    3). refrigerated storage, after 3, 7, 10, and 14 days, and compared to freshly processed
              during
    samples (Figure 3).

                                                              (a)

    Microorganisms 2020, 8, 185                                                                                     9 of 17
                                                              (b)

                                                              (c)
          Figure
     Figure       3. (a)
              3. (a)     Visual
                      Visual      aspect
                              aspect  ofof pineapplecuts
                                         pineapple    cuts during
                                                           during storage.
                                                                   storage.From
                                                                            Fromleft toto
                                                                                  left  right: 0, 3,
                                                                                          right:  0,73,and 14 days
                                                                                                        7 and         of of
                                                                                                                14 days
          storage  at
                    ◦ 4°C;  (b) Olfactive descriptive profiles of minimally-processed  pineapple    stored at
     storage at 4 C; (b) Olfactive descriptive profiles of minimally-processed pineapple stored at 4 C for 0  4  °C◦ for
     days0 (plain
            days (plain
                   line), 3line),
                             days3 (large
                                    days (large dashes),
                                          dashes),  7 days7 (short
                                                            days (short dashes)
                                                                   dashes) or 14or 14 days
                                                                                days         (dotted
                                                                                       (dotted   line);line); (c) PCA
                                                                                                        (c) PCA    analysis
          analysis of olfactive profiles. Sum of F1 and F2 represents 68.24% of data. D0, D3, D7, D14: samples
     of olfactive profiles. Sum of F1 and F2 represents 68.24% of data. D0, D3, D7, D14: samples stored at 4
          stored at 4 °C for 0, 3, 7, and 14 days respectively.
     ◦ C for 0, 3, 7, and 14 days respectively.

         The visual aspect of minimally-processed pineapple clearly turned slightly brown and shiny
     The visual aspect of minimally-processed pineapple clearly turned slightly brown and shiny after
    after 14 days at 4 °C (Figure 3a). K-means classification positioned samples into four classes (Figure
14 days at 4 ◦ C (Figure 3a). K-means classification positioned samples into four classes (Figure 3b).
    3b). Day 0 samples (fresh pineapple) were in class 1. Olfactive descriptors of samples from day 14
Daywere
     0 samples   (fresh pineapple) were in class 1. Olfactive descriptors of samples from day 14 were
          “fermented”, “pungent”, “alcoholic”, “vegetable”, and “milky”. These descriptors indicate a
“fermented”,   “pungent”,   “alcoholic”,
    negative evolution of sensory         “vegetable”,
                                    quality             andover
                                            of the product  “milky”.   Thesecan
                                                                time. They    descriptors
                                                                                be related indicate  a negative
                                                                                            to a previously
    described increase in volatile organic compounds such as ethyl acetate, acetic acid, ethanol or palmitic
    acid during storage of pineapple cuts [19,26]. Significant differences were observed between freshly
    prepared and (class 4) 14-day stored samples. This accounts for “fresh”, “pineapple”, “pungent”, and
    “chemical” descriptors. Samples from day 3 and 7, respectively in classes 2 and 3, were mainly
    characterized by “acid”, “fermented” and “chemical”. PCA analysis showed clearly the differences
    depending on the storage time of samples determined from olfactive descriptors (Figure 3c).
Microorganisms 2020, 8, 185                                                                          10 of 18

evolution of sensory quality of the product over time. They can be related to a previously described
increase in volatile organic compounds such as ethyl acetate, acetic acid, ethanol or palmitic acid during
storage of pineapple cuts [19,26]. Significant differences were observed between freshly prepared and
(class 4) 14-day stored samples. This accounts for “fresh”, “pineapple”, “pungent”, and “chemical”
descriptors. Samples from day 3 and 7, respectively in classes 2 and 3, were mainly characterized by
“acid”, “fermented” and “chemical”. PCA analysis showed clearly the differences depending on the
storage time of samples determined from olfactive descriptors (Figure 3c).
     Depending on the batch, quicker spoilage could be observed (data not shown) and thus analyses
were stopped when a spoilage was observed. For instance, batches TP1, TP2 and TP3, which came
from the same place, were not acceptable after 7 days of storage. Batches BP, CP01, CP02, CP03, CP1,
V0, V1, V2, and V3 were not acceptable after 14 days of storage. The common feature of the latter
batches is that they were all sampled during the summer season. All winter batches, except TP3, were
considered as acceptable after 14 days of storage.
     Changes in physicochemical parameters were determined over the shelf-life of
minimally-processed pineapple (Figure 4 and Figure S1). The values for pH, TA and TSS did not
significantly vary according to storage time. On the opposite side, storage time influenced firmness
and color parameters. A decrease of 26% of firmness was observed after 14 days, when compared
to the determination performed the day of processing. The L* value was not modified according to
storage time, but a* and b* decreased. The calculated dependent parameter C* decreased over storage
time, but h◦ and ∆E did not vary significantly.
     Some physicochemical parameter changes of minimally-processed pineapple during cold storage
have been described [5,7,8,10,12,27–30]. In most of these studies, pH appeared stable or varying by less
than 0.2 units over storage time. For TSS, conflicting results are reported, decreasing [28], stable [27]
or increasing [10] during storage. A gradual decrease in firmness was observed previously [5,10,30].
Changes of color, especially browning, have been described during the shelf-life of minimally-processed
pineapple. A a* value increase was observed during the first 8 days of storage in several studies [10,11,29],
whereas a sharp L* and b* values decrease was observed in other studies [7,10,12,30]. The most
reproducible changes are thus pH and TA stability, firmness decrease and b* decrease, indicating a loss
of the yellow color because of either browning or translucency.
     Counts of psychrotrophic bacteria did not increase during storage time, with mean values of 3.6
to 3.9 log CFU/g at each sampling time (Table 4). This observation hides great differences between
samples, most of samples exhibiting counts below the detection limit and some of them showing
counts up to 6.9 log CFU/g after 10 days of storage. Consequently, a moderate increase of ca. 1.5 log
CFU/g would not have been detected as significant in our experimental conditions. It was showed
that psychrotrophic bacteria counts increased by less than 2 log CFU/g during 12 to 14 days of storage
of pineapple cuts [7,11]. Counts of enterobacteria remained stable at 3.9 log CFU/g during the first
7 days and increased thereafter to reach 4.5 log CFU/g after 14 days of storage (Table 4). The maximal
observed value of enterobacteria counts gradually increased during storage. Lastly, yeast and mold
counts gradually increased during storage time, from initially 4.4 log CFU/g to 5.1 log CFU/g after
7 days and 6.0 log CFU/g after 14 days. Both minimal and maximal yeast and molds counts changed
during storage time to reach respectively 4.0 log CFU/g and 7.6 log CFU/g after 10 days, and 5.0 log
CFU/g and 7.9 log CFU/g after 14 days (Table 4). Significant differences depending on storage duration
were observed for yeast and mold populations.
Microorganisms 2020, 8, 185                                                                                                      11 of 18
      Microorganisms 2020, 8, 185                                                                                         10 of 17

      FigureFigure 4. Values
              4. Values  for for
                             (a) (a) firmness,
                                 firmness,     (b)a*,
                                             (b)   a*,(c)
                                                       (c)b*
                                                           b* and,
                                                              and, (d)
                                                                    (d) C*
                                                                        C*color
                                                                           colorparameters of 25
                                                                                  parameters   of minimally-processed
                                                                                                  25 minimally-processed
            pineapple  batches during   storage at 4°C.
                                                    ◦     Time  of storage varies
      pineapple batches during storage at 4 C. Time of storage varies from 0 (D0),from 0 (D0), 3 (D3), 7 (D7),
                                                                                                  3 (D3),      10 (D10),
                                                                                                           7 (D7),  10 (D10),
            and 14 (D14) days. (+) indicates the mean value, and black dots the outliers. For each parameter,
      and 14 (D14) days. (+) indicates the mean value, and black dots the outliers. For each parameter,
            different uppercase letters indicate significant differences between storage times.
      different uppercase letters indicate significant differences between storage times.
            Some physicochemical
                         Table 4. Changes parameter       changes
                                               in microbial           of minimally-processed
                                                               population      during storage timepineapple
                                                                                                          at 4 ◦ C. during cold
      storage have been described [5,7,8,10,12,27–30]. In most of these studies, pH appeared stable or
            Daysby
      varying     ofless
                     storage                0
                          than 0.2 units over     storage time.  3 For TSS, conflicting
                                                                                      7       results are10 reported, decreasing
                                                                                                                             14
          Number   of samples              25                   25                   22
      [28], stable [27] or increasing [10] during storage. A gradual decrease in firmness was observed   22                  13
      previously [5,10,30].   Microbial
                                Changes counts   in logespecially
                                          of color,     CF/g: mean    (minimumhave
                                                                    browning,      value;been
                                                                                           maximum     value]during the shelf-life
                                                                                                described
      ofPsychrotrophic
         minimally-processed
                         bacteria pineapple.      A a* value
                                     3.7 [3.3; 5.4]            increase
                                                          3.7 [3.3; 5.1] was   3.6observed
                                                                                   [3.3; 6.3] during   the first
                                                                                                   3.9 [3.3; 6.9] 8 days
                                                                                                                       3.7of  storage
                                                                                                                           [3.3; 5.3]
            Enterobacteria
      in several  studies [10,11,29],3.9whereas
                                         [3.0; 5.3] a sharp
                                                          3.9 [3.0;
                                                              L* and6.1] b* values
                                                                               3.9 [3.0; 6.1]
                                                                                     decrease   was4.2observed
                                                                                                       [3.0; 7.0] in other
                                                                                                                       4.5 [3.0; 7.8]
                                                                                                                              studies
           Yeasts and molds         4.4 [3.0; 5.6] A 4.9 [3.5; 6.0] AB        5.1 [3.3;7.4] B    5.5 [4.0; 7.6] BC 6.0 [5.0; 7.9] C
      [7,10,12,30]. The most reproducible changes are thus pH and TA stability, firmness decrease and b*
      decrease, indicating a loss of the yellow color because of either browning or translucency.
     Fungal Counts    of psychrotrophic
               population      was compared bacteria    did3not
                                                     after   days increase   during
                                                                     of storage         storage time,
                                                                                    according     to thewith    mean
                                                                                                            visual     values of
                                                                                                                     spoilage       3.6
                                                                                                                                 observed.
      to 3.9 log  CFU/g     at each sampling      time   (Table   4). This   observation      hides  great
Batches TP1, TP2 and TP3, which appeared spoiled after 7 days of storage, exhibited a fungal population      differences    between
      samples, most of samples exhibiting counts below the detection limit and some of them showing
after 3 days of 5.6 log CFU/g. Batches spoiled after 14 days of storage (BP, CP01, CP02, CP03, CP1, V0,
      counts up to 6.9 log CFU/g after 10 days of storage. Consequently, a moderate increase of ca. 1.5 log
V1, V2, and V3) showed fungal counts of 4.8 log CFU/g after 3 days. The last group of batches, not
spoiled after 14 days of storage, exhibited a mean fungal population after 3 days of 4.8 log CFU/g, and
thus were identical to the latter group. Yeast and mold counts cannot be strictly correlated to shelf-life.
Microorganisms 2020, 8, 185                                                                                             12 of 18

     Mesophilic and psychrotrophic bacteria are possibly involved in minimally-processed pineapple
spoilage, whereas enterobacteria enumerations were used as hygienic indicators of processing. In our
study, the abundance of the two bacterial groups was monitored and did not increase significantly.
The growth of mesophilic and psychrotrophic bacteria in minimally-processed pineapple has been
reported, but consistently to a lesser extent than yeasts and molds [7,10,27,28]. A large and rapid
increase of yeast and mold counts has been previously observed during cold storage of fresh-cut
pineapple [7,10,27,29], confirming our observation. Yeasts and molds are reported as the main
contaminant of fruit salads and fruit juices [31,32]. Yeasts and molds are favored by the high sugar
content and the pH values, comprising between 3.09 and 4.20 for all batches, of minimally-processed
pineapple. They can be responsible for spoilage by producing gas, ethanol and volatile compounds
with off-odors.
     Moreover, we showed that fungal counts cannot be solely used as a spoilage indicator, as they are
not strictly correlated to shelf-life. For that reason, yeast and mold diversity and the relationship to
spoilage was focused on.

3.3. Diversity of Yeasts and Molds and Modulation during Storage
     The profile of yeast and mold communities during refrigerated storage of minimally processed
pineapple was determined to see if differences between samples could be observed. To that aim,
PCR-DGGE analysis was applied to eight batches (Figure 5): CP1 sampled in East area in summer,
VSA sampled in East area in winter, CP03 sampled in the North in summer, V1 sampled in the South
area in summer, V4 and V6 sampled in the South area in winter, and TP1 and TP2 sampled from a local
producer in summer. V1, V4 and V6 originated from the same producer.
       Microorganisms 2020, 8, 185                                                                                 12 of 17

             5. UPGMA
      FigureFigure        dendrogram
                    5. UPGMA             of PCR-DGGE
                                 dendrogram             profiles
                                               of PCR-DGGE       obtained
                                                              profiles      for right
                                                                        obtained   for batches    of minimally-processed
                                                                                        right batches     of minimally-
            processed  pineapple.  D0, D3, D7, D10, and D14 correspond    respectively   to 0,
      pineapple. D0, D3, D7, D10, and D14 correspond respectively to 0, 3, 7, 10, and 14 days  3, 7, 10, and 14 days of
                                                                                                                of storage.
            storage. Letters “a” to “h” label DNA  bands which   were  sequenced.   Arrows     show
      Letters “a” to “h” label DNA bands which were sequenced. Arrows show bands appearing during     bands  appearing
            during
      storage      storage
              and open      and open
                          boxes  bands boxes bands
                                         which     which disappear
                                                disappear           during storage.
                                                          during storage.

            We observed that samples were primarily gathered according to the pineapple batch, rather than
       according to storage time. Three groups were differentiated.
            The first group contained TP1 and TP2 batches that presented only four bands per lane. For these
       two batches, a rapid spoilage occurred and both enterobacteria and yeast and mold counts were
       above 5.5 log CFU/g after 3 days of storage.
            The second group gathered batches V4, CP1 and V6. For those batches, most of the bands were
       observed at the top of the gel. An evolution of the main fungal communities was observed during
       storage, with the appearance (black arrow) or disappearance (empty square) of DNA bands at the
Microorganisms 2020, 8, 185                                                                             13 of 18

      We observed that samples were primarily gathered according to the pineapple batch, rather than
according to storage time. Three groups were differentiated.
      The first group contained TP1 and TP2 batches that presented only four bands per lane. For these
two batches, a rapid spoilage occurred and both enterobacteria and yeast and mold counts were above
5.5 log CFU/g after 3 days of storage.
      The second group gathered batches V4, CP1 and V6. For those batches, most of the bands were
observed at the top of the gel. An evolution of the main fungal communities was observed during
storage, with the appearance (black arrow) or disappearance (empty square) of DNA bands at the
latter storage times (days 10 and 14).
      Lastly, the third group gathered samples CP03, VSA and V1. Their profiles were similar for five
bands, which were labelled “a”, “b”, “c”, “d”, and “g”. The “d” band disappeared from V1 profile after
14 days (Figure 5). DNA retrieved from these bands and sequenced resulted in the identification of (a)
Resinicium saccharicola (mold), (b) Cladosporium sphaerospermum (mold), (c) Cladosporium cladosporioides
(mold), (d) Disporotrichum dimorphosporum (mold), and (g) Rhizopycnis vagum (mold) respectively
(Table 5). The band labelled “h” was only present in V1 sample after 14 days of storage and identified
as belonging to the Rhodotorula glutinis species (pink yeast) (Figure 5 and Table 5). In VSA and V1
groups, two specific bands were labelled “e” and “f”, and were identified as Galactomyces candidum
(mold) and Clavispora lusitaniae (yeast), respectively.

                  Table 5. Identification of fungal species from DNA extracted from DGGE gels.

         Band            Origin             Identification            %Identity            E-Value
           a           CP03–D10         Resinicium saccharicola            98                  0
           b           CP03–D10     Cladosporium sphaerospermum           96.1                 0
           c           CP03–D10      Cladosporium cladosporioides         93.9           4.0 × 10−143
           d            VSA–D0      Disporotrichum dimorphosporum          85             6.0 × 10−8
           e            VSA–D0          Galactomyces candidus             98.8           4.0 × 10−163
           f            VSA–D0           Clavispora lusitaniae            96.4           3.0 × 10−137
           g            V1–D14            Rhizopycnis vagum               95.7           4.0 × 10−146
           h            V1–D14           Rhodotorula glutinis              99            2.0 × 10−86

     Except for TP1 and TP2 coming from the same producer and exhibiting a short shelf-life,
PCR-DGGE grouping was not related to sampling season, neither to the location or producer, as it can
be specifically seen from V1, V4 and V6.
     R. saccharicola was isolated from sugar cane [33]. Cladosporium spp. is widely present on
plant material and can cause post-harvest spoilage of fruit [34–38], even at a low temperature.
D. dimorphosporum is industrially used as a producer of plant cell wall lytic enzymes [39,40]. R.
vagum, infecting roots and tubers, is known to contribute to vine decline and root necrosis [41–43]. G.
candidus, teleomorph of Geotrichum candidum, is mainly derived from cheese [44], but also from fruit tree
phyllosphere [45]. It was identified from necrotic lesions of pineapple [46]. C. lusitaniae was identified
in apple juice and on rotten fruit [47–49]. Rhodotorula spp., corresponding to the “h” band that appeared
in the V1 sample after 14 days of storage, contaminates at high levels fruit salads and juices made from
cantaloupe, citrus, honeydew, strawberry, coconut water, grape, and apple [31,47,48,50]. All detected
fungal species of this study have already been associated to different fruit or plant materials.

3.4. Identification of Fungal Isolates Involved in Spoilage of Minimally-Processed Pineapple
     Nine fungal isolates were obtained from six minimally-processed pineapple batches at different
storage times. Identification is proposed in Table 2. “R” and “S” colony phenotypes were similar
and identified as Penicillium citrinum mold species. Talaromyces amestolkiae was another isolated mold.
Rhodotorula mucilaginosa, Saccharomyces cerevisiae, and Meyerozyma caribbica corresponded to yeast
species isolated. Rhodotorula was the only genus also identified from PCR-DGGE profiles.
3.4. Identification of Fungal Isolates Involved in Spoilage of Minimally-Processed Pineapple
      Nine fungal isolates were obtained from six minimally-processed pineapple batches at different
 storage times. Identification is proposed in Table 2. “R” and “S” colony phenotypes were similar and
 identified as Penicillium citrinum mold species. Talaromyces amestolkiae was another isolated 14mold.
Microorganisms 2020, 8, 185                                                                                                  of 18
 Rhodotorula mucilaginosa, Saccharomyces cerevisiae, and Meyerozyma caribbica corresponded to yeast
 species isolated. Rhodotorula was the only genus also identified from PCR-DGGE profiles.
      P.
      P.citrinum
          citrinumhas  hasbeen
                            beenidentified
                                   identifiedfrom
                                                fromjujube      (Ziziphus mauritiana),
                                                       jujube (Ziziphus     mauritiana), acid
                                                                                            acid food
                                                                                                  food products from citrus,
coco  milk,   coffee   and  cocoa   beans,  in which    its strong  polygalacturonase
 coco milk, coffee and cocoa beans, in which its strong polygalacturonase activity          activity  waswas
                                                                                                           detected   [38,51–54].
                                                                                                               detected   [38,51–
This  fungus
 54]. This        can produce
             fungus                the mycotoxin
                         can produce                  citrinin.
                                          the mycotoxin           Talaromyces
                                                              citrinin.          spp. can
                                                                         Talaromyces     spp.occasionally     be isolated
                                                                                               can occasionally             from
                                                                                                                     be isolated
low-pH     juices juices
 from low-pH         [55,56].[55,56].
                               On theOn opposite,   R. mucilaginosa
                                           the opposite,                and S.and
                                                             R. mucilaginosa     cerevisiae  are commonly
                                                                                      S. cerevisiae            involved
                                                                                                      are commonly         in the
                                                                                                                        involved
spoilage    of fruitofproducts
 in the spoilage                    [48,51,57,58].
                         fruit products              M. caribbica
                                           [48,51,57,58].            is mostly
                                                             M. caribbica        known
                                                                           is mostly       as anas
                                                                                         known     endophyte     yeast,
                                                                                                      an endophyte       but has
                                                                                                                       yeast,  but
been   isolated
 has been          fromfrom
             isolated      spoiled   minimally-processed
                                spoiled    minimally-processed   pineapple    [26,59].
                                                                       pineapple    [26,59].
      Five
      Five isolates
              isolates were selected
                                 selected from
                                            from DNA
                                                   DNAidentification
                                                            identificationand andcolony       morphology:P. P.
                                                                                    colonymorphology:              citrinum
                                                                                                                citrinum      (R),
                                                                                                                           (R),  T.
T. amestolkiae
 amestolkiae        (20),
                (20),      R. mucilaginosa
                       R. mucilaginosa    (A), (A),  S. cerevisiae
                                               S. cerevisiae          (C),M.
                                                               (C), and    and   M. caribbica
                                                                              caribbica          (F).involvement
                                                                                         (F). Their    Their involvement        in
                                                                                                                      in spoilage
spoilage    of minimally-processed
 of minimally-processed            pineapple pineapple
                                                 during during      refrigerated
                                                            refrigerated    storagestorage     was investigated.
                                                                                       was investigated.              Pineapple
                                                                                                               Pineapple     cuts,
cuts,  dipped      in  the  fungal    cocktail  composed       of the  five  isolates,   were   analyzed
 dipped in the fungal cocktail composed of the five isolates, were analyzed and compared to control         and   compared      to
control
 cuts (notcuts   (not dipped)
             dipped)              after of
                          after 7 days   7 days   of storage,
                                            storage,            in triplicate.
                                                       in triplicate.
      Visually,
      Visually,treated
                     treatedcuts
                               cutsappeared
                                     appeareddarker
                                                 darker(Figure
                                                           (Figure6).
                                                                    6). Sensory
                                                                        Sensory triangle tests confirmed the difference,
with
 with a 99.99% confidence. The panel proposed descriptorsof
      a  99.99%      confidence.     The  panel   proposed     descriptors     ofthe
                                                                                  thetreated
                                                                                       treatedsamples:
                                                                                                 samples: These
                                                                                                             These descriptors
                                                                                                                     descriptors
were
 weremainly
        mainlynegative
                   negativeadjectives,
                               adjectives,“fermented”
                                             “fermented”and    and“putrid”
                                                                    “putrid”being
                                                                                beingthethemost
                                                                                             mostfrequent.
                                                                                                    frequent. The
                                                                                                               The descriptors
                                                                                                                     descriptors
“milky”,
 “milky”,“Roquefort
             “Roquefortcheese”,
                              cheese”,then
                                         then“sugared”
                                               “sugared”and   and“toffee”
                                                                   “toffee”werewereless
                                                                                     lessfrequently
                                                                                           frequentlycited.
                                                                                                         cited.

         Figure6.6.Visual
        Figure     Visualaspect
                          aspectof
                                 ofpineapple
                                    pineapplecuts
                                              cutsafter
                                                   after77days
                                                           daysof
                                                                ofstorage
                                                                   storageatat44°C  (left control,
                                                                                ◦ C (left control, right
                                                                                                   right treated).
                                                                                                         treated).

      The comparison of physicochemical parameters pointed to large differences between the control
and the treated samples after 7 days of storage (Table 6). As expected, pH and TSS did not significantly
change. On the opposite, TA decreased during cold-storage of control and increased for the treated
samples after 7 days of storage. Color analysis showed that a* and Hue angle were significantly higher
for the treated samples than for the control conditions. For L*, b*, C*, and ∆E, a bilateral Dunnet’s test
pointed out differences between the treated samples and the control ones after 7 days of storage.

      Table 6. Physicochemical parameters and population of yeast and molds for control and treated
      samples during storage at 4 ◦ C. D0 correspond to freshly prepared pineapple and D7 to samples after 7
      days of storage. Different uppercase letters in the same line indicate significant differences. Lower case
      letters indicate differences according to bilateral Dunnet’s test. *: not applicable.

                       Parameter                    Control—D0              Control—D7              Treated—D7
                         pH                          3.6 ± 0.1 A             3.6 ± 0.1 A             3.5 ± 0.1 A
                    TA (g/100 mL)                    6.1 ± 0.1 B             5.4 ± 0.2 A             6.6 ± 0.2 C
                     TSS (◦ Brix)                   17.1 ± 0.4 A            17.5 ± 0.5 A            16.0 ± 0.2 A
                          L*                          39.5 ± 0.4            39.2 ± 0.8 b            34.6 ± 0.4 b
                          a*                        10.1 ± 0.3 A            10.7 ± 0.4 A            14.2 ± 0.6 B
                          b*                          64.8 ± 0.7            64.0 ± 1.4 b            58.0 ± 0.5 a
                      Chroma                          65.6 ± 0.7            64.9 ± 1.3 b            59.8 ± 0.5 a
                     Hue angle                      8.8 ± 0.3 A              9.5 ± 0.5 A            13.8 ± 0.6 B
                   Color difference                       -*                 1.2 ± 1.1 b             9.4 ± 1.4 a
             Yeasts & Molds (log CFU/g)              4.8 ± 0.2 A            6.1 ± 0.1 AB            10.0 ± 0.1 B
Microorganisms 2020, 8, 185                                                                                   15 of 18

     As expected, the fungal population increased for the control condition during storage, and the
increase was much more marked for the treated sample (Table 6). Colony phenotypes of the five
isolates were observed on enumeration media for the 7-day stored treated samples.

4. Conclusions
     Physicochemical characteristics of minimally-processed pineapple fruit are modulated by the
harvesting season. Hence, microbial populations are probably influenced by composition, together
with environmental conditions. We observed that fungal diversity varied greatly according to the
harvested pineapple batch.
     Olfactive descriptors of minimally-processed ‘Queen Victoria’ pineapple were mostly “fresh”,
“sugared” and “pineapple”. After a 14-day cold-storage, the frequency of descriptors “fermented” and
“alcoholic” increased, as opposed to “pineapple” and “fresh”. At the same time, the fungal population
increased to a large extent, and PCR-DGGE profiles were slightly modified. Identification of yeasts and
molds from PCR-DGGE profiles and from isolates pointed to species already described as associated to
carposphere or fruit foods or beverages, and for some involved in spoilage. The fungal diversity, not
only population level, probably played a crucial role in triggering spoilage.
     A cocktail of two molds and three yeasts was inoculated on pineapple cuts and resulted in sensory
quality defects and color changes. Future research is needed to better link the presence, growth and
activity of fungal species to spoilage, and hence to extend the shelf-life of minimally-processed fruit.

Supplementary Materials: The following are available online at http://www.mdpi.com/2076-2607/8/2/185/s1.
Author Contributions: C.L.-J., J.-C.M. and F.R. performed the conception and experimental design. C.L.-J., B.Q.,
S.A. and M.H. performed the experiments. Data were analyzed by C.L.-J., B.Q., S.A. and F.R. The manuscript was
written by C.L.-J. and F.R. and corrected by all other authors. All authors have read and agreed to the published
version of the manuscript.
Funding: This work was supported by European Union and Region Reunion (FEDER RE0002361). Part of this
work was funded by the Cirad DPP COSAQ (https://cosaq.cirad.fr/) agronomical research program funded by a
grant from European Community (FEDER-working-program), the Regional Council of Réunion Island and CIRAD.
Acknowledgments: The authors thank Stéphane Avril from SCA TERRACOOP-Vivéa and Philippe Roland from
Colipays for providing pineapples.
Conflicts of Interest: The authors declare no conflict of interest.

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